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PROVIDER: PRJEB51811 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:rDNA Region (ITS And rRNA genes for SSU rRNA, ITS1, 5.8S rRNA, ITS2, LSU rRNA (partial)
| PRJEB51814 | ENA
Project description:We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous region-specific binding partners of 45S rRNA in human HCT116 cells. We performed TREX experiments against the full-length 45S, as well as each individual region (5'ETS. 18S, ITS1, 5.8S, ITS2, 28S, and 3'ETS). Extracted proteins from RNase H digested and control cells (4 or 5 replicate per region per condition) were compared, using label-free (LFQ) Quantitative proteomics.
2023-12-27 | PXD044659 | Pride
Project description:Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. By generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.
2025-06-16 | GSE296080 | GEO
Project description:Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a multiphase liquid-like structure where ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps to form the small and large ribosomal subunits (SSU and LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic nucleoli in cells through an engineered rDNA plasmid system, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.
2025-06-17 | GSE296162 | GEO
Project description:In yeast, Upt3 overexpression caused a de-repression of the silenced genes at different loci, suggesting Utp3 might be involved in regulating gene expression. To this end, we extracted total RNA from the WT and sas10 (zebrafish homolg of yeast utp3) embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Comparing the gene expression between the WT and sas10 using DESeq2 identified a total of 8574 differentially expressed genes (DEGs), including 4457 downregulated and 4117 upregulated DEGs in the sas10 mutant (criteria adopted: TPM>5 in at least one replicate, fold-change more than 1.5, p-adjust <0.05). We found that 150 out of 308 liver- and 185 out of 385 intestine-specific genes were identified to be among the downregulated DEGs. GO analysi of upregulated genes showed that these genes are related to protein transport and ribosome biogenesis and function. 64 genes encoding the SSU processome proteins, including wdr36, utp6, tbl3, pwp2h, and utp18 of the UTP-B genes, together with 17 genes encoding the RNA exosome proteins essential for ribosome biogenesis, including mtr4 and dis3 of the RNA Mtr4-exosome genes, were among the upregulated genes in sas10 mutant. By salmon we compared the expression levle of different regions across pre-rRNA transcript, and found that 18S rRNA was significantly decreased, and no obvious difference was observed for ITS1, 5.8S rRNA and 28S rRNA, while 5’ETS and ITS2 was significantly and drastically elevated.
2024-09-18 | GSE244191 | GEO
Project description:Yeast large ribosomal subunit (LSU) precursors are subject to substantial changes in protein composition during their maturation due to coordinated transient interactions with a large number of ribosome biogenesis factors and due to the assembly of ribosomal proteins. These compositional changes go along with stepwise processing of LSU rRNA precursors and with specific rRNA folding events, as revealed by recent cryo-electron microscopy analyses of late nuclear and cytoplasmic LSU precursors. Here we aimed to analyze changes in the spatial rRNA surrounding of selected ribosomal proteins during yeast LSU maturation. For this we combined a recently developed tethered tertiary structure probing approach with both targeted and high-throughput readout strategies. Several structural features of late LSU precursors were faithfully detected by this procedure. In addition, the obtained data let us suggest that early rRNA precursor processing events are accompanied by a global transition from a flexible to a spatially restricted rRNA conformation. For intermediate LSU precursors, a number of structural hallmarks could be addressed which include the fold of the internal transcribed spacer between 5.8S rRNA and 25S rRNA, the orientation of the central protuberance and the spatial organization of the interface between LSU rRNA domains I and III.
2017-04-01 | GSE97276 | GEO
Project description:The multi-layered nucleolus serves as the primary site of ribosome biogenesis, where successive maturation of small (SSU) and large (LSU) ribosomal subunit precursors occur. However, the spatio-functional relationship between pre-rRNA processing and nucleolar substructures and how this adapts to changing cellular physiological demands have remained incompletely understood. Here, our spatiotemporal analyses revealed a compartment-specific ribosomal subunit processing in human nucleoli, with SSU processomes maintained in fibrillar center/dense fibrillar component/periphery dense fibrillar component (FC/DFC/PDFC) domains while LSU pre-rRNAs largely transited to PDFC/granular component (GC) regions. Slow proliferating cells exhibited unexpected 5' external transcribed space (5' ETS)-centered SSU processing impairment, accompanied by FC/DFC structural remodeling and retarded SSU outflux. Direct 5' ETS processing perturbation at least partially recapitulated these FC/DFC alterations, supporting the functional interdependence between SSU processing and nucleolar architecture. Notably, anamniote bipartite nucleoli with merged FC/DFC compartments, exhibited distinct 5' ETS distribution and slower pre-rRNA flux compared to multi-layered nucleoli in amniotes. Introducing a FC/DFC interface to bipartite nucleoli enhanced processing efficiency, indicating that evolutionary emergence of nested FC/DFC may have optimized pre-rRNA processing. Collectively, depicting the spatiotemporal distribution of pre-rRNAs revealed an essential role of 5' ETS-centered SSU processing in maintaining nucleolar substructures and suggested a possible evolutionary advantage of the multi-layered structure in amniotes.
2025-07-22 | GSE301874 | GEO
Project description:The eukaryotic ribosome biogenesis is a highly orchestrated multistep process that starts at the nucleolus with the transcription of pre-rRNAs 5S and 35S. The latter comprises the mature 18S, 5.8S and 25S rRNAs separated by internal transcribed spacers (ITS1 and ITS2) and externally flanked by the 5’ETS and 3’ETS. The 35S pre-rRNA undergoes several co- and post-transcriptional processing events, which will enable the pre-60S and pre-40S particles to take independent maturation routes. Hundreds of assembly factors (AF) are required, being recruited and released hierarchically, for the proper folding of the rRNAs and correct positioning of the ribosomal proteins. One of the most intricate events that have recently been described is the removal of the ITS2-containing structure called pre-60S foot, which happens in a step-wise manner. Nop53 is an essential 60S AF that binds close to the ITS2 and plays a fundamental role in recruiting the RNA exosome for the 7S pre-rRNA processing, thereby dismantling the foot structure. Here we characterize the impact of Nop53 binding to the pre-60S on the compositional changes that happen during 60S assembly. For this purpose, preribosomes were affinity-purified with TAP-tagged 60S AFs (Nop7, Erb1, Rsa4, Arx1, Nmd3, Yvh1, and Lsg1) representative of different maturation stages both in the presence and absence of Nop53. Nop7 particles were also coimmunoprecipitated in the presence of Nop53 mutants incapable of recruiting the exosome (Nop53∆1-71, Nop53∆48-98) to compare with Nop53 depletion. The isolated preribosomes were analyzed by label-free MS/MS-based quantitative proteomics, revealing early and late-stage specific effects of Nop53 depletion.
2021-09-09 | PXD023383 | Pride
Project description:- Biscogniauxia sp. strain SG25 internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence - >Biscogniauxia sp. strain SG25 large subunit (LSU), contains 28S rRNA gene partial sequence, complete D1/D2 region nrDNA sequence
| PRJEB32032 | ENA
Project description:- Daldinia sp. strain SG1 internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence - Daldinia sp. strain SG1 large subunit (LSU), contains 28S rRNA gene partial sequence, complete D1/D2 region nrDNA sequence
| PRJEB32030 | ENA